twaddlac

# Command I use to build the image
# docker buildx build --build-arg CONDA_PACKAGES=./envs/nsap_packages.txt --platform linux/amd64 -t alantwaddle/nsap_test:1.6 --push .

# (c) 2012 Continuum Analytics, Inc. / http://continuum.io
# All Rights Reserved

# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#     * Redistributions of source code must retain the above copyright
#       notice, this list of conditions and the following disclaimer.

twaddlac

## To get back all of the primary screen first pass interesting experiment images for Amalia and Victoria

## Select the fields of interest
SELECT 
    s.screen_name,
    # a.assay_code_name,                       # the assay itself (not needed, redundant with library plate coordinates)
    a.assay_image_path,
    l.ReagentName,                             # the reagent used
    l.MasterPlateWell, l.StockPlateWell,       # library coordinates for the reagent
    # m.treatment_group_id,                    # treatment group (ignore for now)

twaddlac

# get JUST the image file paths for
# matching RNAi controls for "FIRST-PASS INTERESTING" 
# from am and vi screens (12 and 14)

SELECT b.assay_image_path

FROM  exp_assay a, 
      exp_assay b,  
      exp_design d,
    exp_manual_scores AS m,

twaddlac

select 
experiment.well,
experiment.worm_strain_id,
experimentplate.temperature,
experimentplate.date,
experiment.library_stock_id,
wormstrain.*,
librarystock.*,
experiment.*,
experimentplate.*,

twaddlac

Chain INPUT (policy ACCEPT)
target     prot opt source               destination
delegate_input  all  --  anywhere             anywhere

Chain FORWARD (policy ACCEPT)
target     prot opt source               destination

Chain OUTPUT (policy ACCEPT)
target     prot opt source               destination

twaddlac

select 
	experiment.well,
	experiment.worm_strain_id,
	experimentplate.temperature,
	experimentplate.date,
	experiment.library_stock_id,
	wormstrain.*,
	librarystock.*,
	experiment.*,

twaddlac

import xml.etree.ElementTree
import re

root = xml.etree.ElementTree.parse('RNAi.fixed.xml').getroot()
pattern = re.compile("\w")

def get_text_list(child,path):
    l = list()
    for i in child.findall(path):
        if pattern.match(i.text):

twaddlac

# This defines the language that you're script is written int - most likely it's always bash/sh.
#!/bin/sh

#SBATCH --job-name=filter_abund
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=12
#SBATCH --mem=24GB
#SBATCH --time=72:00:00
#SBATCH --mail-type=ALL
#SBATCH --mail-user=twaddlac@gmail.com

twaddlac

#!/bin/sh
module load trimmomatic

cd /scratch/at120/gabby-laura-stats/

# for i in $(ls *fastq | perl -pe 's/\.fastq//g'); do mv $i.fastq $(echo $i | perl -pe 's/^C.+l0(\d)n0(\d)_(.+)\.3.+/$3_l$1.r$2.fastq/g'); done

# for i in $( ls *fastq | perl -pe 's/\.r\d\.fastq//g' | sort | uniq); do sbatch --export=fastq=$i trimmomatic.sh ; done
java -jar /share/apps/trimmomatic/0.36/trimmomatic-0.36.jar PE -threads 12 $fastq.r1.fastq $fastq.r2.fastq -baseout $fastq.fastq ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

twaddlac

�
module load trimmomatic

cd /scratch/at120/gabby-laura-stats/

# for i in $(ls *fastq | perl -pe 's/\.fastq//g'); do mv $i.fastq $(echo $i | perl -pe 's/^C.+l0(\d)n0(\d)_(.+)\.3.+/$3_l$1.r$2.fastq/g'); done

java -jar /share/apps/trimmomatic/0.36/trimmomatic-0.36.jar PE -threads 12 $fastq.r1.fastq $fastq.r2.fastq -baseout $fastq.fastq ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36